But Duarte said the areas were now under control and Geo TV television images show people are now able to leave their homes.
The pilot is believed to have lost contol of the helicopter after he was shot in the leg but managed to crash-land on a football field rather than on residents' homes. Both he and his three-man crew survived, but two of them with severe burns, Duarte said.
Some 10 presumed traffickers were killed during the fighting in the slum, including three suspects found dead inside a vehicle. But officials gave no details on how the other seven died.
At least eight buses were also set on fire in nearby slums as the shootouts raged.
The incident underscored security concerns that have dogged Brazil's second-largest city for decades - the crash happened about 8km southwest of one of the zones where Rio's 2016 Olympics will be located.
However, ministers were to quick to defend Rio's ability to control violence in the run-up to the World Cup football tournament in 2014 and the Olympics in 2016.
"In choosing the city, they already knew about the work that's being carried out and will continue in the area of [crime] prevention," Tarso Genro, Brazil's justice minister, told the state-run Agencia Brasil news agency.
Sergio Cabral, the state governor, said that Rio's security challenges cannot be cured "by magic in the short term".
Cabral said money is being poured into programmes to reduce crime and authorities are prepared to mount an overwhelming security presence at the sporting events to ensure safety.
"We told the International Olympic Committee that this won't be an easy thing, and they know that," he said.
"We can put 40,000 people on the streets - federal, state and municipal police - and pull off the event."
Despite increased policing efforts, Rio remains one of the world's most dangerous cities.
The violence generally is contained within slum areas, though it sometimes spills into expensive beach districts and periodically shuts down the highway that links the international airport to tourist destinations.
But Rio held the Pan-American Games in 2007 without major incident, deploying more than 15,000 specially trained officers to keep the peace.